Publications

* Equal contributors

# Co-senior authors

† Correspondence

Li Lab members are highlighted in bold.

(2020). Thousands of Novel Unannotated Proteins Expand the MHC I Immunopeptidome in Cancer. bioRxiv.

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(2020). A Single-Cell and Single-Nucleus RNA-Seq Toolbox for Fresh and Frozen Human Tumors. Nature Medicine.

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(2020). Linking Indirect Effects of Cytomegalovirus in Transplantation to Modulation of Monocyte Innate Immune Function. Science Advances.

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(2020). Integrated scRNA-Seq Identifies Human Postnatal Thymus Seeding Progenitors and Regulatory Dynamics of Differentiating Immature Thymocytes. Immunity.

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(2019). Cumulus: A Cloud-based Data Analysis Framework for Large-scale Single-Cell and Single-Nucleus RNA-seq. bioRxiv.

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(2019). Accuracy Assessment of Fusion Transcript Detection via Read-Mapping and De Novo Fusion Transcript Assembly-based Methods. Genome Biology.

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(2019). Decoding Human Fetal Liver Haematopoiesis. Nature.

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(2019). Nuclei Multiplexing with Barcoded Antibodies for Single-Nucleus Genomics. Nature Communications.

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(2017). STAR-Fusion: Fast and Accurate Fusion Transcript Detection from RNA-Seq. bioRxiv.

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(2016). Metrics for Rapid Quality Control in RNA Structure Probing Experiments. Bioinformatics.

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(2015). Perm-seq: Mapping Protein-DNA Interactions in Segmental Duplication and Highly Repetitive Regions of Genomes with Prior-Enhanced Read Mapping. PLoS Computational Biology.

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(2014). Evaluation of de novo Transcriptome Assemblies from RNA-Seq Data. Genome Biology.

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(2013). De novo Transcript Sequence Reconstruction from RNA-seq using the Trinity Platform for Reference Generation and Analysis. Nature Protocols.

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(2011). Discoevering Transcription Factor Binding Sites in Highly Repetitive Regions of Genomes with Multi-Read Analysis of ChIP-Seq Data. PLoS Computational Biology.

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(2010). RNA-Seq Gene Expression Estimation with Read Mapping Uncertainty. Bioinformatics.

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